For the Sitecore Solr Support package, a work around at the moment is you could rename the zip locally to Sitecore 8.1 rev. 151120.zip (so the tool thinks this is a CMS package).
The single DLL nuget packages would be generated for those DLLs then.
As there are third party DLLs in there, as you mentioned, have a look into finding the third party packages for them instead.
With my pull request, I left the parameter there for legacy, but believe it shouldn't be used. You don't want Newtonsoft.Json.DLL to end up in two different packages... that'll lead you down Nuget hell.
But for the third party DLLs without associated packages (as listed here gist.github.com/.../d0f3b2adfff0acd9fc78
), maybe there is some reason for it. I wonder how often these DLLs are used in development though? Are there any that you use as references in your code?